R/bayesnec-package.R

In AIMS/bayesnec: A Bayesian No-Effect- Concentration (NEC) Algorithm

#' The 'bayesnec' package.
#'
#' @description A No-Effect toxicity estimation package that uses brms (Bürkner 
#' (2018), https://github.com/paul-buerkner/brms) to fit concentration
#' (dose)-response data using Bayesian methods for the purpose of estimating
#' both Effect Concentration (ECx) values, but more particularly 'NEC'
#' (Fox 2010), 'NSEC' (Fisher and Fox 2023), and 'N(S)EC (Fisher et al. 2023).
#' A full description of bayesnec can be found in Fisher et al. (2024).
#' Please see ?bnec for more details. This package expands and supersedes an
#' original version implemented in R2jags (Su and Yajima 2020), see Fisher et
#  al. (2020).
#' @docType package
#' @name bayesnec-package
#' @aliases bayesnec
#' @importFrom ggplot2 autoplot
#' @importFrom brms bernoulli Beta negbinomial beta_binomial
#'
#' @references
#' Bürkner P-C (2018) Advanced Bayesian Multilevel Modeling with the R Package
#' brms. The R Journal, 10: 395-411. doi:10.32614/RJ-2018-017.
#' 
#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
#' Concentration-Response Modeling and Estimation of Toxicity Metrics
#' doi:10.18637/jss.v110.i05.
#' 
#' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
#' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
#' doi: 10.1002/etc.5610.
#'
#' Fisher R, Fox DR, Negri AP, van Dam J, Flores F, Koppel D (2023). Methods for
#' estimating no-effect toxicity concentrations in ecotoxicology. Integrated 
#' Environmental Assessment and Management. doi:10.1002/ieam.4809.
#' 
#' Fisher R, Ricardo GF, Fox, DR (2020) jagsNEC: A Bayesian No Effect
#' Concentration (NEC) package. doi:10.5281/ZENODO.3966864.
#' 
#' Su Y, Yajima M (2020). R2jags: Using R to Run 'JAGS'. R package version
#' 0.6-1, <https://CRAN.R-project.org/package=R2jags>.
#' 
#' Fox DR (2010). A Bayesian Approach for Determining the No Effect
#' Concentration and Hazardous Concentration in Ecotoxicology. Ecotoxicology
#' and Environmental Safety, 73(2), 123–131. doi: 10.1016/j.ecoenv.2009.09.012.
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